.. DO NOT EDIT.
.. THIS FILE WAS AUTOMATICALLY GENERATED BY SPHINX-GALLERY.
.. TO MAKE CHANGES, EDIT THE SOURCE PYTHON FILE:
.. "examples_gallery/mkh5/append_cals.py"
.. LINE NUMBERS ARE GIVEN BELOW.
.. only:: html
.. note::
:class: sphx-glr-download-link-note
Click :ref:`here <sphx_glr_download_examples_gallery_mkh5_append_cals.py>`
to download the full example code
.. rst-class:: sphx-glr-example-title
.. _sphx_glr_examples_gallery_mkh5_append_cals.py:
append separate cals
====================
.. GENERATED FROM PYTHON SOURCE LINES 7-9
Set up
-------
.. GENERATED FROM PYTHON SOURCE LINES 9-18
.. code-block:: default
from pathlib import Path
from matplotlib import pyplot as plt # for inspecting cal pulses
from mkpy import mkh5
MKDIG_PATH = Path("../mkdig_data")
print("mkpy version", mkh5.__version__)
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
mkpy version 0.2.7
.. GENERATED FROM PYTHON SOURCE LINES 19-25
Create subject, append cals
---------------------------
Use :meth:`mkh5.append_mkdata()<mkpy.mkh5.mkh5.append_mkdata>` to
combine EEG recordings and separately recorded calibration data in
a single .h5 file prior to converting A/D samples to :math:`\mu` V.
.. GENERATED FROM PYTHON SOURCE LINES 28-29
Set EEG and calibration data file names
.. GENERATED FROM PYTHON SOURCE LINES 29-37
.. code-block:: default
crw = MKDIG_PATH / "sub000p3.crw" # EEG recording
log = MKDIG_PATH / "sub000p3.x.log" # events
yhdr = MKDIG_PATH / "sub000p3.yhdr" # extra header info
cals_crw = MKDIG_PATH / "sub000c.crw"
cals_log = MKDIG_PATH / "sub000c.log"
cals_yhdr = MKDIG_PATH / "sub000c.yhdr"
.. GENERATED FROM PYTHON SOURCE LINES 38-39
Convert .crw/.log to mkh5 format .h5.
.. GENERATED FROM PYTHON SOURCE LINES 39-44
.. code-block:: default
p3_h5_f = "example_sub000p3.h5"
p3_h5 = mkh5.mkh5(p3_h5_f)
p3_h5.reset_all()
p3_h5.create_mkdata("sub000", crw, log, yhdr)
.. GENERATED FROM PYTHON SOURCE LINES 45-46
Append calibration data to the existing ``sub000``.
.. GENERATED FROM PYTHON SOURCE LINES 46-48
.. code-block:: default
p3_h5.append_mkdata("sub000", cals_crw, cals_log, cals_yhdr)
.. GENERATED FROM PYTHON SOURCE LINES 49-51
Convert EEG and calibration data A/D to microvolts.
set re-usable calibration parameters
.. GENERATED FROM PYTHON SOURCE LINES 51-59
.. code-block:: default
cal_kws = dict(
n_points=5, # samples to average
cal_size=10, # uV
lo_cursor=-36, # lo_cursor ms
hi_cursor=48, # hi_cursor ms
cal_ccode=0, # condition code
)
.. GENERATED FROM PYTHON SOURCE LINES 60-61
inspect the calibration pulses
.. GENERATED FROM PYTHON SOURCE LINES 61-64
.. code-block:: default
f, ax = p3_h5.plotcals(p3_h5_f, "sub000", **cal_kws)
plt.show()
.. image-sg:: /examples_gallery/mkh5/images/sphx_glr_append_cals_001.png
:alt: calibration pulses (recorded N=209) from: example_sub000p3.h5 sub000 n_points=5 cal_size=10 lo_cursor=-36 hi_cursor=48 cal_ccode=0, scale=17.63, trimmed 4, scale=20.30, trimmed 6, scale=20.05, trimmed 2, scale=20.79, trimmed 5, scale=20.57, trimmed 2, scale=40.10, trimmed 5, scale=39.59, trimmed 9, scale=40.74, trimmed 25, scale=40.41, trimmed 12, scale=39.97, trimmed 5, scale=38.81, trimmed 16, scale=35.54, trimmed 12, scale=36.47, trimmed 6, scale=40.55, trimmed 10, scale=37.84, trimmed 13, scale=39.66, trimmed 9, scale=42.00, trimmed 11, scale=39.58, trimmed 7, scale=41.42, trimmed 5, scale=40.46, trimmed 18, scale=40.05, trimmed 22, scale=40.76, trimmed 12, scale=40.66, trimmed 3, scale=39.91, trimmed 13, scale=40.58, trimmed 12, scale=40.35, trimmed 14, scale=40.75, trimmed 21, scale=41.24, trimmed 12, scale=40.69, trimmed 8, scale=40.91, trimmed 8, scale=20.56, trimmed 23, scale=20.64, trimmed 10
:srcset: /examples_gallery/mkh5/images/sphx_glr_append_cals_001.png
:class: sphx-glr-single-img
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
Plotting cals
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/mkh5.py:3666: UserWarning: negative event code(s) found for cal condition code 0 -16384
warnings.warn(msg)
Found cals in /sub000/dblock_4
.. GENERATED FROM PYTHON SOURCE LINES 65-66
Convert EEG and calibration data A/D to microvolts.
.. GENERATED FROM PYTHON SOURCE LINES 66-67
.. code-block:: default
p3_h5.calibrate_mkdata("sub000", **cal_kws)
.. rst-class:: sphx-glr-script-out
Out:
.. code-block:: none
/usr/share/miniconda/envs/env_3.8/lib/python3.8/site-packages/mkpy/mkh5.py:3666: UserWarning: negative event code(s) found for cal condition code 0 -16384
warnings.warn(msg)
Found cals in /sub000/dblock_4
Calibrating block /sub000/dblock_0 of 5: (31232,)
Calibrating block /sub000/dblock_1 of 5: (32768,)
Calibrating block /sub000/dblock_2 of 5: (31744,)
Calibrating block /sub000/dblock_3 of 5: (32512,)
Calibrating block /sub000/dblock_4 of 5: (28416,)
.. rst-class:: sphx-glr-timing
**Total running time of the script:** ( 0 minutes 7.960 seconds)
.. _sphx_glr_download_examples_gallery_mkh5_append_cals.py:
.. only :: html
.. container:: sphx-glr-footer
:class: sphx-glr-footer-example
.. container:: sphx-glr-download sphx-glr-download-python
:download:`Download Python source code: append_cals.py <append_cals.py>`
.. container:: sphx-glr-download sphx-glr-download-jupyter
:download:`Download Jupyter notebook: append_cals.ipynb <append_cals.ipynb>`
.. only:: html
.. rst-class:: sphx-glr-signature
`Gallery generated by Sphinx-Gallery <https://sphinx-gallery.github.io>`_